[gmx-users] Questions about protein simulations.
quantrum75 at yahoo.com
Wed Jul 15 17:36:47 CEST 2009
Dear Gromacs users,
Hi I wanted to ask a begnniner's question regarding protein MD. I have prior experience with MD simulations through simulating lipid systems. However I beginning to do some protein MD simulations and wanted the anyone's advice regarding the forcefields to be used for proteins.
1) Is OPLS-AA the standard for protein simulations using GROMACS? I havent seen that many papers using OPLS-AA Gromacs for protein simulations as I have seen say AMBER or CHARMM. In fact I have also seen a CHARMM port for GROMACS making me wonder if there is somthing wrong with using OPLS-AA for proteins. Any advice or pointers in this direction would be very helpful. Any pitfalls regarding the same? My protein is pretty much a standard protein without any funny amino acids or additional molecules.
2) Water model - which is the best model to use....TIP or SPC? why would one choose one versus another for protein simulations?
3) Scientific resources for decent protein simulations in GROMACS? I have read some of Van Der Spoel s publications, but they are more in the nature of optimizing protein simulations rather than running basic applied ones. Put in another way, i am more interested in the applied aspect of the protein simulations rather than the optimization of the same.
I understand these are basic questions. But I'd grateful for sage and cogent replies.
Thanks to the group for the wonderful service rendered.
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